The move was hailed by a Christian group which said the gesture "both respects and acknowledges an alternative viewpoint" on the origins of the earth. But after facing criticism for including theories that the planet is only 6,000 years old, the Trust said it had merely acknowledged the presence of such views and was committed to scientific evidence on the origins of the Causeway.
The issue of including creationist theories has sparked controversy in the past in Northern Ireland, when prominent members of the Democratic Unionist Party at Stormont lobbied for museums to include such opinions.
The Causeway is a Unesco World Heritage Site and features more than 40,000 interlocking basalt columns formed millions of years ago by volcanic activity.
The Trust said the new £18.5 million centre, opened by First Minister Peter Robinson and Deputy First Minister Martin McGuinness on Tuesday, showcased the science and the stories of the Giant's Causeway.
A National Trust spokesman said: "The interpretation in the visitor centre showcases the science of how the stones were formed, the history of this special place and the stories of local characters. We reflect, in a small part of the exhibition, that the Causeway played a role in the historic debate about the formation of the earth, and that for some people this debate continues today.
"The National Trust fully supports the scientific explanation for the creation of the stones 60 million years ago. We would encourage people to come along, view the interpretation and judge for themselves."
The interactive exhibition in question includes an audio package re-enacting debates between historic figures, who argued over the origins of the Causeway, as well as their contrasting biblical and scientific beliefs on the origins of the planet.
The exchanges end with a further clip stating: "This debate continues today for some people, who have an understanding of the formation of the earth which is different from that of current mainstream science. Young Earth Creationists believe that the earth was created some 6,000 years ago. This is based on a specific interpretation of the Bible and in particular the account of creation in the book of Genesis.
"Some people around the world, and specifically here in Northern Ireland, share this perspective. Young Earth Creationists continue to debate questions about the age of the earth. As we have seen from the past, and understand today, perhaps the Giant's Causeway will continue to prompt awe and wonder, and arouse debate and challenging questions for as long as visitors come to see it."